Apple Pie Thumbprint Cookies – tender and chewy almond shortbread cookies filled with a sweet and spiced homemade apple pie filling, just like Panera Bread!
Have you been to Panera Bread yet to try their irresistible apple almond thumbprint cookies? They aren’t exactly pretty but in this case, looks are deceiving because these cookies are DELICIOUS. Apple pie + almond shortbread cookies are a match made in heaven.
Ever fell in love with something on a menu only to find out it’s a seasonal limited-time offer, never to be seen again? It’s literally the worst. I couldn’t risk losing these cookies, so I bought a few and got to work developing this copycat Panera recipe.
My version of Panera’s apple almond thumbprint cookies isn’t an exact match. However, these might even be better. I’m obsessed with these cookies and I am totally making them every fall! I hope that you make them and love them as much as I do. Enjoy.
Tips & Tricks
- I start with the filling. It may seem tedious but dice the apples as small as you can. You want the filling to have some texture, but the pieces need to be small enough to fit in the cookie wells.
- You can make the apple pie filling and store it in the fridge until you’re ready to fill the cookies. If you are really feeling it, double the apple pie filling and use the other half for spooning over ice cream, vanilla yogurt, or stirring into your morning oatmeal.
- I like my pie filling to be really spiced, so I am heavy-handed with the pie spice.
- As with any type of cookie dough, be careful not to overmix the dough. You want a tender cookie, not a tough one.
- When I first made these, I wasn’t crazy about the texture. However, I loosely covered them with plastic wrap, and the next morning they were perfect. That said, be sure to loosely cover the cookies with plastic wrap and let sit overnight before eating. The texture will be perfect the next day.
Why are Apple Pie Thumbprint Cookies So Good?
- These cookies fuse all of the flavors and textures of homemade apple pie into a bite-size indulgent cookie.
- Thumbprint cookies are a great addition to your holiday cookie baking list. They’re perfect for gifting and bringing to gatherings.
- Made with simple ingredients yet packed with sweet, spiced, and cozy flavors.
- Simple. Making thumbprint cookies is easier than it looks.
Thumbprint Cookie Filling Variations
When it comes to thumbprint cookie flavors, the options are endless. In addition to this apple pie filling, almond thumbprint cookies are great filled with:
- Raspberry Jam
- Orange Marmalade
- Strawberry Preserves
- Chocolate Sauce
- Caramel Sauce
- Peanut Butter & Grape Jelly
How to Store
Storing: Store thumbprint cookies in an airtight container for up to a week at room temperature. The cookies will stray fresh for up to a week before they lose their moisture and become dry.
Make-Ahead and Freezer Options
Freezing: To freeze almond thumbprint cookies, freeze the shortbread cookie without the filling. You can add the filling once the cookies have thawed out.
Why did my thumbprint cookies go flat?
If there isn’t enough flour in the dough to absorb the fat and moisture, your cookies will spread too much and become flat. Be sure to measure out the flour precisely or better yet, weigh the flour to ensure you’re using the right amount.
Should you fill thumbprint cookies before or after baking?
I recommend filling the cookies immediately after they are finished baking. You may need to gently re-indent the cookie.
Apple Pie Thumbprint Cookies
Ingredients
Apple Pie Filling:
- 2 apples peeled and cut into a small dice
- 1 Tablespoon lemon juice
- 2 teaspoons pie spice
- ⅓ cup sugar
- 2 Tablespoons butter
- 1 teaspoon water
- 1 teaspoon cornstarch
- 1 teaspoon vanilla bean paste or extract
Almond Thumbprint Cookies:
- 1 cup almond flour
- 3 ½ cups flour
- ½ teaspoon salt
- 1 ½ cups butter room temperature
- 1 cup sugar
- 1 teaspoon almond extract
- 1 teaspoon vanilla bean paste or extract
Instructions
- Make the apple pie filling: In a large mixing bowl, add diced apples, lemon juice, pie spice, and sugar. Toss to coat apples and combine.
- Cook apples: In a large pan, over medium heat, melt the butter. When the butter has melted, add the coated apples to the pan and cook, stirring frequently, until the apples begin to caramelize and appear glossy (10 to 15 minutes). If the butter dries up, add a splash of water and continue cooking.
- Add cornstarch: In a small bowl, mix together a teaspoon of water and corn starch. If the pan is dry, add a teaspoon or two more of water. Then, add the corn starch mixture. Stir well.
- Finish and cool: Bring the apple pie filling to a boil, cook for an additional 30 seconds to 1 minute to activate the cornstarch, and then stir in the vanilla. Transfer mixture to a bowl and let cool completely.
- Preheat and prep baking sheet: Preheat the oven to 350 degrees F. Line two baking sheets with parchment paper and set aside.
- Mix dry ingredients: In a medium mixing bowl, add almond flour, flour and salt. Whisk well to combine. Set aside.
- Mix wet ingredients: In the bowl of an electric mixer, add butter, sugar, almond extract and vanilla. Mix until smooth and well combined..
- Mix almond shortbread cookie dough: To the bowl with the wet ingredients, add the dry ingredient mixture and mix on low until the flour is just incorporated and the dough forms. Do not overmix.
- Shape cookies: Using a rounded tablespoon, shape the dough into rounded balls and place on the prepared baking sheet, leaving at least an inch in between each ball. Press your thumb into the center of each ball of dough, creating a well for the apple pie filling. If the dough cracks, just gently press it back together.
- Bake and finish cookies: Transfer the baking sheet to a preheated 350-degree oven and bake for 18 to 24 minutes or until the dough has been set but not yet browned. Allow the cookies to cool completely before filling each well with apple pie filling. Dust with powdered sugar (optional) and enjoy.
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